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US 2026/0066041 A1Published application
Detecting mutational signatures with k-mer-based pseudoalignment
AssigneeCalifornia Institute of Technology
InventorsJoseph M. Rich, Lior S. Pachter, Laura Luebbert, Delaney Sullivan
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Abstract
Disclosed herein include systems, devices, methods, and computer readable media for reference-based mutation or variant detection. The detection can be based on an index of variant-containing reference sequences and k-mer-based psuedoalignment.
Claims27
A method for determining one or more variants:
- under control of a hardware processor
- receiving variant information of a plurality of variants and an associated reference;
- generating a plurality of variant-containing reference sequences (VCRSs) from the variant information of the plurality of variants and an associated reference;
- building an index of the plurality of VCRSs;
- receiving a plurality of sequence reads obtained from a sample;
- and
- determining one or more variants present in the plurality of sequence reads using the index of the plurality of VCRSs.
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A system for determining one or more variants comprising:
- non-transitory memory configured to store executable instructions and a plurality of variant-containing reference sequences (VCRSs), wherein the plurality of VCRSs is generated from variant information of a plurality of variants and an associated reference;
- and
- a hardware processor in communication with the non-transitory memory, the hardware processor programmed by the executable instructions to perform:
- receiving a plurality of sequence reads obtained from a sample;
- and
- determining one or more variants present in the plurality of sequence reads using the plurality of VCRSs.
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Dependencies are inferred from the claim text.